map_cnv {oncoPredict}

This function maps cnv data to genes. The output of this function is a .RData file called map.RData; this file contains theCnvQuantVecList_mat (rows are genes, and columns are samples) and tumorSamps (indicates which samples are primary tumor samples, 01A).

Description

This function maps cnv data to genes. The output of this function is a .RData file called map.RData; this file contains theCnvQuantVecList_mat (rows are genes, and columns are samples) and tumorSamps (indicates which samples are primary tumor samples, 01A).

Usage

map_cnv(Cnvs)

Arguments

Cnvs

The cnv data. A table with the following colnames: Sample (named using the TCGA patient barcode), Chromosome, Start, End, Num_Probes, and Segment_Mean.

Value

A .RData file called, map.RData, which stores two objects: theCnvQuantVecList_mat (rows are genes, columns are samples), tumorSamps (indicates which samples are primary tumor/01A). This output will serve as the input for test().